We report the development of a frequency domain second harmonic OCT system. The system uses a 170 fs pulses from Yb fiber laser and second harmonic spectrum is recorded by a 0.17 nm resolution spectrometer and thermoelectric cooled CCD detector. The system is applied to image biological tissue of the fish scales. Highly organized collagen fibrils can be visualized in the recorded images. The axial resolution of the frequency domain SH-OCT is 30 μm.

We have developed a novel imaging technique, ground state recovery pump-probe optical coherence tomography (gsrPPOCT), which measures the transient absorption and recovery time of the ground state of a target chromophore or chromophores. By imaging the molecular absorption as opposed to the fluorescence of the target contrast agent, gsrPPOCT helps to fill a valuable niche for imaging biologically important molecules which do not fluoresce. The majority of biologically active molecules are non fluorescent. Here we present gsrPPOCT imaging of natural and transfected chromophores in living animal and plant tissues, as well as the first gsrPPOCT measurements of the ground state recovery time of a molecular chromophore, which may be used to deduce the relative concentrations of a mixture of chromophores.

Use of indocyanine green (ICG), an FDA-approved dye, in a pump-probe scheme for optical coherence tomography (OCT) is reported. Aqueous solutions of ICG are not stable, i.e., the dye degrades over time especially in the presence of light. Addition of protein such as bovine serum albumin (BSA) stabilizes the ICG; however, when exposed to high intensity illumination, the dye still degrades. Moreover, the photodegradation is permanent and occurs swiftly if the illumination band corresponds to the ICG absorption peak. The permanence of the photobleached state illustrates that ICG photobleaching phenomenon has great potential to achieve contrast in OCT. ICG solutions with 50 micromolar concentration were prepared in water, 1% BSA, and 0.8% agarose to study the dynamics of the dye for different illumination intensity levels. In addition, different molar concentrations of ICG in water were studied for fixed illumination intensity. In each case, probability of photobleaching, defined as the ratio of the total photobleached ICG molecules to the total photons absorbed by the ground-state molecules, is evaluated to characterize the photobleaching phenomenon in ICG. We also demonstrate ICG-based pump-probe MCOCT imaging by mapping the distribution of ICG in a stage 54 Xenopus laevis.

Our first steps towards nanoparticle assisted, optical molecular imaging (NAOMI) using OCT as the imaging modality are presented. We derive an expression to estimate the sensitivity of this technique. We propose to use nanoparticles based on biodegradable polymers, loaded with suitable dyes as contrast agent, and outline a method for establishing their desired optical properties prior to synthesis. This report presents preliminary results of our investigation on the use of nanoshells to serve as contrast agents We injected nanoshells with specific contrast features in the 800 nm wavelength region in excised porcine eyes. The nanoshells showed up as bright reflecting structures in the OCT images, which confirm their potential as contrast agents.

In this manuscript we describe the design and optimization of ultrahigh resolution spectral/Fourier domain OCT systems for three applications in retinal imaging: imaging of the normal retina, three-dimensional (3D) imaging of retinal pathologies, and 3D imaging of the rodent retina. Seven spectrometer configurations were tested for resolution and sensitivity drop with depth, and CCD pixel crosstalk was characterized. The human retina was imaged in vivo with five different axial resolutions between 2 and 10 microns, and with three different transverse resolutions. Information from these experiments enabled the optimization of OCT systems for the above applications. Results include clinical 3D data of retinal pathologies, high quality cross-sectional images of the normal retina with different axial and transverse resolutions and 3D data from the rat and mouse retinas. Factors affecting the sensitivity fall-off are discussed and theoretical predictions are compared with experimental measurements. Different retinal imaging applications necessitate different system designs, depending on the requirements of speed, axial resolution, axial measurement range, transverse resolution, and field of view. While axial resolution is the dominant factor in image quality, a smaller transverse spot size can reduce speckle size and improve contrast at boundaries such as the boundary between the ganglion cell layer and the inner plexiform layer. The effect of reducing the transverse spot size is most pronounced in images with 5-10 um axial resolution. In addition, we characterize all factors responsible for the sensitivity drop with depth in spectral/Fourier domain OCT.

Adaptive optics-optical coherence tomography (AO-OCT) has the potential to improve lateral resolution for OCT retinal
imaging. Several reports have already described the successful combination of AO with a scanning confocal Fourier-domain
OCT instrument to permit real-time three-dimensional (3D) imaging with high resolution (in all three
dimensions). One of the key components that sets the performance limit of AO is the wavefront corrector. Several
different wavefront correctors have been used in AO-OCT systems so far. In this paper we compare two commercially
available wavefront correctors: an AOptix Bimorph deformable mirror (DM) and a Boston Micromachines Micro-
Electro Mechanical System (MEMS) DM (used for the first time in an AO-OCT system). To simplify the analysis, we
tested their performance for the correction of low-amplitude high-order aberrations (with minimal defocus and
astigmatism). Results were obtained with an AO-OCT instrument constructed at UC Davis that combines state-of-the-art
Fourier-domain OCT and an AO design to allow simultaneous testing of both mirrors without the need to modify the
optical system.

Spectral-Domain Optical Coherence Tomography (SDOCT) allows for in-vivo video-rate investigation of biomedical tissue depth structure intended for non-invasive optical diagnostics. It has been suggested that OCT can be used for di-agnosis of glaucoma by measuring the thickness of the Retinal Nerve Fiber Layer (RNLF). We present an automated method for determining the RNFL thickness from a 3-D dataset based on edge detection using a deformable spline algo-rithm. The RNFL thickness map is combined with an integrated reflectance map and retinal cross-sectional images to provide the ophthalmologist with a familiar image for interpreting the OCT data. The video-rate capabilities of our SDOCT system allow for mapping the true retinal topography since motion artifacts are significantly reduced as com-pared to slower time-domain systems. Combined with Doppler Velocimetry, SDOCT also provides information on retinal blood flow dynamics. We analyzed the pulsatile nature of the bidirectional flow dynamics in an artery-vein pair for a healthy volunteer at different locations and for different blood vessel diameters. The Doppler phase shift is determined as the phase difference at the same point of adjacent depth profiles, and is integrated over the area delimited by two circles corresponding to the blood vessels location. Its temporal evolution clearly shows the blood flow pulsatile nature, the cardiac cycle, in both artery and vein. The artery is identified as having a stronger variation of the integrated phase shift. We observe that artery pulsation is always easily detectable, while vein pulsation seems to depend on the veins diameter.

The authors report preliminary clinical results using an unique instrument which acquires and displays simultaneously an OCT image, a confocal image similar to that of a scanning laser ophthalmoscope and an indocyanine green fluorescence image. The three images are produced by three channels, an OCT and a confocal channel operating at 793 nm and a confocal channel tuned on the ICG fluorescence spectrum, which peaks at 835 nm. The system is based on our previously described ophthalmic Optical Coherence Tomography (OCT)/confocal imaging system, where the same source is used to produce the OCT image and excite fluorescence in the ICG dye. The system is compact and assembled on a chin rest and it enables the clinician to visualise the same area of the eye fundus in terms of both en-face OCT slices and ICG angiograms, displayed at the same time. The images are collected by fast T-scanning (en-face) which are then used to build B-scan or C-scan images.

Despite the great advantages of spectral domain (SD) OCT in terms of sensitivity and imaging speed, the technology has still a drawback: the instantaneous recording of an entire A-scan prevents dynamic focusing and therefore high transversal resolution throughout a larger imaging depth. Time domain (TD) OCT, on the other hand, records its data only from a single depth at one instant, thus allowing to match the depth position of focal point and coherence gate by synchronous movement over the entire image depth. Transversal TD scanning patterns are especially suited for dynamic focus tracking because the rather slow progression of the coherence gate alleviates the mechanical demands on precise synchronous focus movement. We have implemented a dynamic focus tracking into our previously reported transversal TD retinal OCT system. A lens in the scanning optics is moved synchronously with the coherence gate with a predetermined velocity profile. B-scan and C-scan images of the retina are recorded in 0.5 to 1 sec. We demonstrate the method by imaging a USAF test resolution target in a model eye and a retina of a healthy volunteer in vivo. High transverse resolution and signal intensity are demonstrated throughout an imaging depth of 1 - 2 mm.

We report a versatile imaging system combining scanning laser ophthalmoscopy (SLO) and T-scan based en face ultrahigh resolution optical coherence tomography (OCT). The image carrier is generated using the optical path difference modulation introduced by the X-Y galvo-scanner mirrors specific to en face OCT (without optical modulators in the reference arm). The light source is a compact superluminescent diode based source with 150 nm FWHM spectrum, centered at 890 nm. We demonstrate en face B-scan and C-scan ultrahigh resolution OCT imaging of the human retina in vivo, with an axial resolution of 3.2 μm in tissue. The system is capable of acquiring large lateral size ultrahigh resolution OCT scans of a maximum field size of 20°. The acquisition speed is up to 2 frames/s for both OCT B-scans and C-scans. The measured system sensitivity is more than 98 dB, for a power level to the target of 1 mW and maximum lateral scan size. The C-scans are, to the best of our knowledge, the first and the largest size reported ultrahigh resolution C-scans of the human retina in vivo. The instrument is assembled on a chin rest and ready to be used for clinical imaging. SLO and ultrahigh resolution OCT C-scans are acquired simultaneously and displayed side by side. This allows users in a clinical environment to correlate details of the same feature in the area of interest in both images and also choose precisely in the SLO image the location where to perform the ultrahigh resolution en face B-scan.

A versatile time-domain OCT system is presented which, for the first time, can generate cross-section images (B-scans) by using either transverse priority (T-scans) or depth priority (A-scans). Images from the optic nerve are obtained with either regime, with the same system. In different scanning regimes, different values are allowed for the maximum power to be launched to the eye. We present the maximum exposure level for a variety of scanning procedures, such as generation of cross section images and 3D volumes employing either A or T scanning.

We are developing computer-aided diagnosis (CAD) algorithms to aid in the classification of dysplasia in Barrett's esophagus (BE) using endoscopic OCT (EOCT). Our previous CAD algorithm yielded single spatial scale texture features, used a single parameter as a classifier, and used only one EOCT image per biopsy site. In this work, we aim to overcome these limitations. We present progress in development of Fourier domain fractal analysis with classification trees using multiple images to classify a single site for more accurate dysplasia classification in BE EOCT images. A total of 812 EOCT images (13 patients, 70 non-dysplastic biopsy sites including 499 images and 38 dysplastic biopsy sites including 313 images) were analyzed. Using only one frame for classification, 95% sensitivity (95% confidence interval (CI) is 82%-100%) and 94% specificity (95% CI is 86%-98%) were achieved. Using three frames per biopsy site and requiring two frames to be positive to classify the site as positive, 100% sensitivity (95% CI is 89%-100%) and 100% specificity (95% CI is 94%-100%) were achieved, and 97% of the sites had at least three frames available. In conclusion, Fourier domain fractal analysis with classification tree achieved more successful classification of dysplasia in BE than our previous CAD algorithm. And making use of multiple images from a single biopsy site can improve the accuracy of classification. CAD has the potential to enable EOCT surveillance of large surface areas of Barrett's mucosa for dysplasia.

This paper summarizes the development of new 2D MEMS mirrors and the pertinent modification to improve OCT endoscopic catheter packaging suitable for in vivo imaging diagnosis of bladder cancers. Comparative study of the newly developed endocopic OCT versus the bench-top OCT is presented. Results of in vivo OCT cystoscopy based on a porcine acute inflammation model are presented to compare time-domain OCT and spectral-domain OCT for in vivo imaging. In addition, results of spectral-domain Doppler OCT are presented to image blood flow in the lamina propria of the bladder. The results of our in vivo animal study using the presented OCT endoscope are discussed for potential problems in the future clinical applications.

The post-genomic promise of a plethora of new therapeutic drugs has remained largely unfulfilled because of two principal bottlenecks: insufficient high-throughput drug toxicity assays, and acceptable in vitro surrogates to in vivo testing. In this paper, we report coherence-domain functional imaging of bulk tissue response to drug toxicity using cellular motility as both a contrast agent for imaging and as a biomarker for metabolic activity. Osteogenic sarcoma tumor spheroids treated with sodium azide exhibit a rapid onset of increased cellular motility, followed by cellular exhaustion. This behavior correlates with the known biological progression of azide poisoning. These specific findings for azide poisoning are relevant in general because of the common action of many drug candidates on the same oxidative phosphorylation pathways affected by azide. Furthermore, azide poisoning is generally representative of hypoxia, including ischemic hypoxia, which is the most common cause of tissue damage in disease and trauma. The OCI motility mapping technique could therefore introduce a new and general approach to the study of toxicity and pathology in vitro.

A fluorescence-image-guided OCT (FIG-OCT) system is described, and its ability to enhance the sensitivity and specificity is examined in an animal bladder cancer model. Total 97 specimens were examined by fluorescence imaging, OCT and histological microscopy. The sensitivity and specificity of FIG-OCT is 100% and 93% respectively, compared to 79% and 53% for fluorescence imaging, while the OCT examination time has been dramatically decreased by 3~4 times. In combination of endoscopic OCT, FIG-OCT is a promising technique for effective early bladder cancer diagnosis.

Fourier Domain Optical Coherence Tomography (SD-OCT) systems for dental measurements are demonstrated. Two systems have been developed. The first system is fiber based Michelson interferometer with super luminescent diodes at 1310 nm and 100 nm FWHM as a light source. The sensitivity of the system was 106 dB with depth measurement range in air of 2.5 mm. The second systems is a fiber based Mach-Zehnder interferometer with wavelength scanning laser as light source at center wavelength of 1310 nm, wavelength range of 110 nm and scanning rate of 20 KHz. The sensitivity of the system is 112 dB and depth measurement range in air is 6 mm. Both systems can acquire real-time three dimensional (3-D) images in the range of several second. The systems were applied for early caries detection in tooth, for diagnostics of tooth condition after operational tooth treatment, and for diagnostics of the alveolar bone structure. In-vivo measurements were performed on two volunteers. The systems were able to detect discontinuities in tooth and resin filling after tooth treatment. In addition early carries lesion was detected in one of the volunteers. The 3-D profile of the alveolar bone was acquired for first time with non-contact method.

The use of optical coherence tomography (OCT) as a monitoring tool in the growth of human fibroblasts cells in collagen-based constructs is investigated. Rat-tail tendon type-1 collagen based gels mixed with human fibroblasts were prepared and incubated. Fixed samples were then imaged using OCT, and subsequently cross-sectioned and analysed
microscopically. The concentration of cells in samples under different contraction dynamics was investigated using analysis of the OCT images. Results show clear differences in scattering intensity as a consequence of cell concentration in both OCT images and micrographs.

Dynamic optical coherence tomography (OCT) is demonstrated for dynamic study of sweat glands of human finger tip using the all-optical-fiber imaging system. Stress-induced and physical activation of sweat glands can be observed clearly in time-sequential OCT images. The method for image data acquisition is presented as well as the experimental results.

We measure an extracted tooth by OFDR-OCT. Three-dimensional reconstruction is performed against OCT images. Non-telecentric scanning is reproduced in three-dimensions and refractive image distortions are corrected by ray tracing.

A two- and three- dimensional swept source optical coherence tomography (SS-OCT) system which uses a ready-to-ship scanning light source is demonstrated. The light source has the center wavelength of 1.31 μm, the -3 dB wavelength range of 110 nm, the scanning rate of 20 KHz and high linearity of frequency scanning. A simple calibration method using a fringe analysis technique for spectral rescaling is presented. This SS-OCT is capable of realtime display of two-dimensional OCT, and can take three-dimensional OCT with the measurement time of 2 s. In vivo human anterior eye segments are investigated both two- and three- dimensionally. The system sensitivity is experimentally determined as 113 dB.

Fourier domain optical coherence tomography (FDOCT) is a high speed imaging technique with high axial resolution in
the micro-meter-scale range combined with a high sensitivity allowing to probe 3D volumes of weakly back-scattering
biological tissues in-vivo. Phase shifting techniques allow the reconstruction of the full complex sample signal which
results in an additional suppression of unwanted auto-correlated distortion as well as an extended depth range. Current
complex FDOCT realizations introduce the phase shift via reference path length modulation causing chromatic phase
errors especially if broad bandwidth light sources are employed. Broad optical bandwidth is necessary for ultrahigh
resolution OCT systems. By frequency shifting the light fields with acousto-optic frequency shifters in the reference and
sample arm respectively, a phase-resolved signal at high speed can be registered. Therefore the reference arm does not
rely on arm length changes or delays. The beating signal generated this way shows high phase stability. The phase of this
beating signal is not wavelength-dependent, as the frequency shift applied is the same for all wavelengths. With a
Ti:Sapphire laser at 800nm and a spectral width of 130nm a high speed complex FDOCT system is realized with an axial
resolution of 4μm.

We have developed a new algorithm and configuration for removing the autocorrelation of the object wave in spectral optical coherence tomography. The self-interferogram of the object wave is acquired synchronously with the standard interferogram of the recombined object and reference waves. The former is then subtracted from the latter after Fourier transformation. The algorithm is validated by numerical simulation and by experimental measurement of a USAF target and a feline eye.

A high-speed line-field Fourier-domain optical coherence tomography system has been developed. Tomographic images consisting of 656 A-lines are obtained at 121 frames per second. It is corresponding to 79,400 A-line/s. Three-dimensional volume sets consist of 256 OCT images are measured within 2.1 seconds. The sensitivity of this system is 79.5 dB. A biological tissue measurement is demonstrated with human nail fold in vivo. The three-dimensional nail fold structure is visualized.

We present a simple processing technique that uses the concept of minimum-phase functions to improve frequency-domain optical coherence tomography systems. Our novel approach removes the auto-correlation noise and therefore increases both the accessible depth range and the recovery accuracy. Furthermore it provides a better axial resolution. To our knowledge, this is the first time that the concept of minimum-phase functions has been applied to improve optical coherence tomography.

In this article we present a novel approach to quantitative imaging by Fourier domain optical coherence tomography. Using an eigenanalysis technique, a matrix model of the sample under test is fitted to real spectral data to extract layer dependent refractive index and thickness values. We demonstrate this method experimentally for a simple test artefact, made from silica test slides and highly scattering dental composite.

A numerical deconvolution method that cancels the blurring due to lateral defocus in line field Fourier domain optical coherence tomography (LF-FDOCT) using imaging optics is proposed. This method employs an inverse filter designed from the point spread function (PSF) that is calculated by Fresnel diffraction. The inverse filter can eliminate the lateral defocus, and consequently, the out-of-focus lateral resolution can be improved to a level comparable with the in-focus resolution over the entire axial measurement range. In this paper, we describe the process of calculating the PSF and the inverse filter designed from it in LF-FDOCT. The effect of deconvolution is also schematically discussed and estimated. A knife-edge method also verifies the effect of in-focus resolution experimentally.

We demonstrate a high-speed tuneable, continuous wave laser source at 1550nm for Fourier domain OCT imaging. The light source was based on a pigtailed semiconductor optical amplifier and a diffraction grating and polygon mirror for fast frequency tuning. This source provides frequency scan rate of up to 20kHz over a wavelength range of 80nm (60nm FWHM) at the central wavelength of 1550nm, offering an axial resolution of ~17 microns.

A method of lateral superresolution for Fourier domain optical coherence tomography is presented. This method consists of intentional defocus and its numerical compensation using a spatial frequency- phase filter. The designing process of the phase filter is described, and the superresolution effect is discussed theoretically. Experimental results of a knife-edge test prove that the frequency filter enhances the lateral resolution better than a diffraction-limited resolution. This method is applied to the investigation of an in vivo human iris and shows the effect of the cancellation of defocus.

Recently, Fourier domain optical coherence tomography (FDOCT) has attracted much attention due to the significantly improved sensitivity and imaging speed compared to time domain OCT. The large depth of focus is necessary to image a long-depth-range sample with constant transverse resolution in FDOCT where dynamic focusing is not considered. Under such imaging scheme, an axicon lens can be used instead of a conventional focusing lens in the sample arm of OCT to achieve both high lateral resolution and a long depth of focus simultaneously. In this study, a 800μm diameter axicon lens was fabricated on a silica wafer. We incorporated the fabricated axicon lens into the sample arm of our FD OCT system and investigated the lateral resolution over a long depth range, compared to the same FD OCT system using a conventional lens.

Techniques based on spectral interferometry (SD-OCT) have recently been examined, with authors often suggesting
superior performance compared to time domain optical coherence tomography (TD-OCT) techniques. While these
technologies have similar resolutions and the spectral techniques may currently claim faster acquisition rates, their
detection parameters may be inferior. This work examines the theoretical signal to noise ratio and dynamic range of
these techniques including time domain. Considering the practical limits of optoelectronics, the often ignored or
misunderstood factors which affect performance, such as vacuum fluctuations, the actual source of thermal noise,
excess noise and A/D conversion losses, were taken into account. Methods for potentially improving signal to noise
ratio (SNR), such as fast laser sweeping with high laser intensities and CCD integration, were evaluated as well. This is
critical because dynamic range translates directly into imaging depth. The technologies are compared relative to the
differences in these parameters. While Fourier domain OCT (FD-OCT) has some advantages such as signal integration,
it appears unlikely that its disadvantages can ultimately be overcome. Ultimately, time TD-OCT appears to have the
superior performance with respect to SNR and dynamic range. However certain positive aspects of swept source OCT
(SS-OCT) leave open the possibility that its performance may approach that of TD-OCT.

We have constructed an integrated optical microscope that allows for the simultaneous image acquisition from multiple optical imaging modalities. The microscope consists primarily of hardware for spectral-domain optical coherence microscopy (OCM), multi-photon microscopy (MPM), and second harmonic generation microscopy. The unique configuration of the integrated microscope allows for the acquisition of both anatomical and functional imaging information with particular emphasis in the fields of tissue engineering and tumor biology. By overlaying the structural image obtained from OCM on the functional image obtained simultaneously from MPM (i.e., fluorescent markers imply functional proteins), a more comprehensive view of different tissues can be obtained. In addition, the contemporary analysis of the spectroscopic features enhances contrast in OCM by differentiating different cell and tissue components.

Holographic Optical Coherence Imaging (OCI) uses spatial heterodyne detection in direct analogy with the temporal heterodyne detection of time-domain OCT. The spatial demodulator can be a sensitive dynamic holographic film or can be a CCD array placed directly at the hologram plane. We show that a digital hologram captured at the Fourier plane requires only a simple 2D inverse FFT of the digital hologram to compute the real image and its conjugate. Our recording on the optical Fourier plane has an advantage for diffuse targets because the intensity distribution of diffuse targets is relatively uniform at the Fourier plane and hence uses the full dynamic range of CCD camera. We applied this technique to human liver tumor spheroids and produced depth-resolved images to depth of 1.4 mm.

An imaging fibre bundle is demonstrated for spatially-multiplexed probe beam delivery in OCT, with the aim of eliminating the mechanical scanning currently required at the probe tip in endoscopic systems. Each fibre in the bundle addresses a Fizeau interferometer formed between the bundle end and the sample, allowing acquisition of information across a plane with a single measurement. Depth scanning components are now contained within a processing interferometer external to the completely passive endoscope probe. The technique has been evaluated in our laboratory for non-biological samples. Images acquired using the bundle-based system are presented. The potential of the system is assessed, with reference to SNR performance and acquisition speed.

We present a three-dimensional (3-D) endoscopic optical coherence tomography (OCT) system based on a dual axis microelectromechanical system (MEMS) mirror. The diameter of MEMS mirror was 1.2 mm and both axes were capable of scanning up to 20° (optical) at greater than 1 kHz with excellent linearity. The MEMS mirror was packaged in a machined acrylic endoscopic housing which provided mechanical protection and electrical interconnects as well as optical alignment of the MEMS device to a focusing GRIN lens. The endoscopic MEMS probe was integrated and tested with both a fiber-based time domain (TD) OCT system and Fourier domain (FD) OCT system. Combining the 2-axis lateral scanning of the MEMS device with an axial scan allowed 3-D volume images to be obtained at a rate of 3 frames/s for the TD system and 7 frames/s for the FD system. In the initial investigations, in vivo 3-D OCT images of a human finger as well as images of animal tissue such as healthy rabbit trachea, normal and cancerous regions of hamster cheek pouch tissue were obtained. These images allowed real-time diagnosis of diseased tissue and also clearly delineated important features and tissue structures.

We propose a novel forward-imaging OCT needle probe. The probe is based on the use of two angled GRIN lenses that can freely rotate with respect to each other. The probe is capable of scanning a forward cone volume ahead of the probe tip. Different scanning modes, such as the conventional OCT B-scan mode, spiral mode and starburst B-scan mode, can be obtained by adjusting the angular scan velocities of the two GRIN lenses. We develop a prototype probe and demonstrate its capability to acquire OCT images. In this paper we give the characteristics of the prototype probe and display images of different part of tadpole acquired by the probe. The longitudinal resolution, lateral resolution and the signal-to-noise ratio of the system are 10 μm, 10 μm and 93 dB, respectively.

We have modeled, fabricated, and tested polyimide amplified piezoelectric bimorph scanning mirrors for application in optical coherence tomography (OCT). These scanning mirrors are fabricated using photolithography using polyimide as a substrate. These devices use bimorph actuators to drive polyimide micromechanical structures at resonance. The forced vibration of these micromechanical structures causes polysilicon gold plated mirrors attached to two torsion hinges to tilt. Operating the device at resonance allows us to achieve very large displacements of the mirror at real-time imaging speeds. The large scan angles and fast imaging speeds give these novel scanning devices the potential to be used to image larger areas of tissue to search for diseases such as mucosal cancers and to guide interventional procedures such as laser ablations and biopsies in real time. The mirror and support structures were modeled using one-dimensional beam theory and fundamental vibration mechanics. The structures were also modeled and simulated using ANSYS, a finite element analysis package. The finite element modeling has also lead to the development of new methods to fabricate the entire devices on a single silicon wafer. Prototype scanning devices have demonstrated optical scan angles up to 97 degrees with applied voltages from 15-60 V at a resonant frequencies ranging from 12-60 Hz, appropriate for real time imaging. These amplified bimorph imaging probes have been integrated into the scanning arm of a Spectral Domain OCT (SD-OCT) imaging system and have been used to generate preliminary in vivo human skin images at frame rates of 25 frames per second.

A semiconductor laser with an external fiber cavity based on quantum-well superluminescent diode and tunable acousto-optic filter is investigated. The-tuning range of 60nm, instant linewidth below 0.1 nm and output power of several mW ex SM fiber are obtained. Sweep frequency of up to 200 Hz is demonstrated. The prototype of a portable light source of this kind is manufactured.

We implemented a fiber-based optical coherence tomography (OCT) system by using a photonic crystal fiber (PCF) coupler which could support an ultra-wideband spectral bandwidth. The PCF coupler fabricated by the fused biconical tapered (FBT) method showed rather flat coupling efficiency over a broad spectral bandwidth. Furthermore, the mode-field shapes at the output ports of the PCF coupler showed single mode characteristic over a wideband range. These features will enable the OCT system to operate at 1300 nm as well as at 800 nm without changing the coupler. The FWHM of the interferogram was measured to be about 3 um when a white-light source was used. While a Ti:Sapphire laser and a conventional superluminescent diode (SLD) produced interferograms with FWHMs of about 4 um and 15 um, respectively. The OCT imaging performance of the PCF-based OCT system was demonstrated by imaging an in vitro rat eye and Misgurnus mizolepis skin with a SLD source at 1300 nm and by imaging a tooth with a Ti:Sapphire laser source at 800 nm. The PCF coupler might enable the utilization of an ultra-wideband supercontinuum generated light source in fiber-optic OCT systems for obtaining high resolution, and also realization of a white-light source as a cost effective solution for fiber-based high-resolution OCT systems. Further, this coupler also can operate as single mode not only near 1000 nm but also near 500 nm wavelengths. This feature may support realization of fiber based second harmonic (SH) OCT system.

A new technique utilizing harmonic Fourier spectra created by the non-linear properties of a compact Fourier transform infrared interferometer (FTIR) was proposed and realized to improve the system resolution. The compact standing wave FTIR (SWFTIR) system consists of a partial transparent hetero-junction bipolar phototransistor (HPT) and a free scanning highly reflective mirror. The overall size of the system is less than 5×5×5cm3, and the resolution at 1.5μm is better than 37.5cm-1 at the 5th harmonic spectral component. The SWFTIR array system has theoretical resolution of better than 1cm-1 covering the whole near-infrared region with potential compact portable applications.

A 1310nm superluminescent diode (SLED) has been demonstrated with > 80mW continuous wave (CW) output power at 25 0C with a spectral bandwidth of > 60nm and peak-to-peak modulation of < 0.6dB. Low power ( ~ 4 mW), ultrawide bandwidth ( ~ 95nm) SLED can also be realized using the same structure but shorter cavity length.

We demonstrate a novel technique to determine the size of Mie scatterers with high sensitivity. Our technique is based on spectral domain optical coherence tomography measurements of the dispersion that is induced by the scattering process. We use both Mie scattering theory and dispersion measurements of phantoms to show that the scattering dispersion is very sensitive to small changes in the size and/or refractive index of the scatterer.

An object structure can be better resolved in optical coherence tomography by using inverse scattering theory, which
takes into account the finite beam width and focusing. Specifically, we show experiments where scatterers are
resolved outside of the confocal region such that resolution is uniform to the focused region. Numerical simulations
demonstrate the effectiveness of this technique. When the algorithm is applied to experimentally-acquired OCT data,
the transverse resolution outside of the confocal parameter is improved, extending the apparent confocal parameter
range. The experimental results validate improvement for capabilities of OCT to perform high-resolution cross-sectional
imaging.

Despite many efforts, some tissue changes, associated with diseases such as cancer, remain beyond the detection limit of OCT. A technique which would allow extraction of information regarding these unresolvable features from the OCT signal could prove a very powerful diagnostic tool. This manuscript presents such a procedure. It begins with the separation of the signal in resolvable and unresolvable components using wavelet decomposition. Subsequently, the power spectral density of the unresolvable part is determined with autoregressive spectral estimation. Analysis is then employed to extract information regarding the uresolvable, but diagnostically significant, scatterers in tissue. These characteristics could considerably improve the clinical utility of OCT.

The influence of an angular spectrum of light fields (formed by extended light sources or at sharp focusing using high numerical apertures) on the signal of a low-coherence interferometer is discussed. The reduction of amplitude of the interferometer signal at probing of layered object owing to a broad angular spectrum has been shown both experimentally and by computer modeling.

We present a full-field phase microscopy technique, motivated by swept-source Fourier-domain optical coherence tomography, for quantitative nanoscale two-dimensional profiling of sample surfaces and internal structures. The optical configuration consisted of a common path interferometer, illuminating the sample with a collimated beam and detecting the back-scattered light on a 2D CCD camera. A tunable fiber Fabry Perot filter was used to sweep a narrow band (0.07nm) through the 47nm FWHM bandwidth of a superluminescent diode source. The full field of view was recorded for each discrete wavelength step, generating a spectrally indexed interferometric data cube mapping each pixel to a point on the sample. A three dimensional volume was generated by performing the discrete Fourier transform along the spectral axis. Sub-coherence length variation across a depth slice was obtained by examining the phase of the Fourier transformed data set at the selected depth. The phase stability of the system was measured to be 1.3nm for high SNR surface features. The nanoscale imaging potential of this system was demonstrated by measuring the height of patterned chrome on a USAF resolution target, the location of receptor sites on a DNA assay biochip, and the surface topography of erythrocytes in a blood smear.

A swept source based Fourier domain optical Doppler tomography (FDODT) system was developed. The technique is based on a phase resolved method where phase information was retrieved from the reconstructed complex fringe signals. The aliasing effects and artifacts caused by lateral scanning and sample movement were removed with a signal processing technique. The standard deviation of the phase shift of the system was reduced from 49 to 1.8 degree with the signal processing method employed. Structural and Doppler images of fluid flow through glass channels were quantified and blood flow through vessels of chick chorioallantoic membrane (CAM) were demonstrated in vivo.

As the imaging speed of Optical Coherence Tomography (OCT) and Optical Doppler Tomography (ODT) increases, a
new horizon to access dynamical systems with fast transients will be open near future. The objective of this research is
to demonstrate its potential to measure simultaneously the structure and velocity information of dynamical systems.
Transient two-fluid mixing in microfluidic devices are good examples to display clearly the advantages of ODT over
other techniques. Laminar dispersion in a serpentine microchannel with a Y-shape inlet was investigated using OCT and
ODT. It was shown that OCT/ODT is not only a visualization method but also a methodology to characterize important
physics: streamwise velocity, secondary streamline, sedimentation time scale, shear dispersion. To demonstrate the
capability of OCT/ODT, transient mixing was observed and three-dimensional imaging was performed.

A variation on the standard time domain optical coherence tomography (TDOCT) system is presented. Using an inexpensive piezoelectric stack to modulate the reference mirror position, the amplitude and phase of the sample reflection is determined without scanning. With the primary scan in the transverse direction, en face and B-scan OCT images can be readily produced with phase information. This project plans to use the dynamic phase information to add an extra level of contrast to the images, based on the motion of the scatterers.

Since the advent of Adaptive Optics in ophthalmic instrumentation, several attempts for improving the performances of the existing observing techniques, either in imaging or tomography, have been made. For long, Adaptive Optics have proven its ability to restore high lateral resolution with the SLO or flood imaging, or more recently to enhance the interferometric contrast and hence, the sensitivity, of OCT. Nevertheless, the direct acquisition of en face tomographic images equivalent to horizontal optical sections of the retinal tissue is still the objective of intensive developments. We report here a new instrumental approach where a time domain full field OCT setup has been coupled with a double pass adaptive optics system, providing 300 x 300 x 4 μm instantaneous optical sections of biological tissues. We will describe how the interferometric contrast is derived without any modulation of the optical path, thus giving access to targets as critical, because unstable, as the retinal tissue during in vivo ophthalmic examinations. The advantages of this new design, which benefits from the implementation of very recent deformable mirrors, featuring simultaneously a higher actuators density and a much larger stroke, will be discussed, and the ability of the system to accommodate for variable pupil sizes, thanks to wavefront sensing techniques optimized for ophthalmology, are commented. The performances of the system, in terms of X,Y,Z resolution, sensitivity, registration capability and / or image stabilisation are discussed and illustrated with results obtained in the laboratory and in clinical environment.

Since blood flow is tightly coupled to the health status of biological tissue, several instruments have been developed
to monitor blood flow and perfusion dynamics. One such instrument is laser speckle imaging (LSI). The objective of
this work is to evaluate an LSI instrument employing two statistically based approaches to calculate the speckle flow
index (SFI). To study the relation between SFI and the actual flow rate for the two statistical approaches, speckle
images were acquired from a 0.5% blood filled tube embedded within a 5 mm thick agar gel. A syringe based infusion
pump was used to inject the blood at flow rates between 0 and 5 mm/sec. We found a linear relationship between SFI
and actual flow rate for both the Gaussian and Lorentzian based approaches. With the Gaussian based approach, the
SFI dynamic range was up to six times larger than with the Lorentzian based approach. The Gaussian based approach
is a good alternative for computation of SFI using LSI.

We present the first demonstration of measurements of velocity and direction of flow using Transversal Doppler Optical
Coherence Tomography. The experiments are carried out using a four-channel quadrant detector at the output of a freespace
Michelson interferometer. This allows real three dimensional mapping of both flow and velocity with no
limitation on the Doppler angle.

Birefringence of skeletal muscle has been associated with the ultrastructure of individual sarcomeres, specifically the arrangement of A-bands corresponding to the thick myosin filaments. Murine skeletal muscle (gastrocnemius) was imaged with a fiber-based PS-OCT imaging system to determine the level of birefringence present in the tissue under various conditions. In addition to muscle controls from wild-type mice, muscle from abnormal mice included: genetically-modified (mdx) mice which model human muscular dystrophy, transgenic mice exhibiting an overexpression of integrin (α7β1), and transgenic integrin (α7β1)knockout mice. Comparisons were also made between rested and exercised muscles to determine the effects of exercise on muscle birefringence for each of these normal and abnormal conditions. The PS-OCT images revealed that the presence of birefringence was similar in the rested muscle with dystrophy-like features (i.e., lacking the structural protein dystrophin - mdx) and in the integrin (α7β1)knockout muscle when compared to the normal (wild-type) control. However, exercising these abnormal muscle tissues drastically reduced the presence of birefringence detected by the PS-OCT system. The muscle exhibiting an overexpression of integrin (α7β1) remained heavily birefringent before and after exercise, similar to the normal (wild-type) muscle. These results suggest that there is a distinct relationship between the degree of birefringence detected using PS-OCT and the sarcomeric ultrastructure present within skeletal muscle.

A high speed polarization sensitive spectral domain optical coherence tomography setup has been developed. The system retrieves the backscattered intensity, birefringence, and optic axis orientation with only one A-scan per measurement location. The setup was used to image the polarization properties of the human retina at the fovea and the optic nerve head region, and the polarization properties of the anterior eye segment.

Development of endoscope-compatible fiber-optic probes and polarization-sensitive detection schemes have each independently expanded the utility of optical coherence tomography. Several application areas have emerged which require polarization-sensitive measurements to be combined with endoscopic imaging techniques, in order to proceed to in vivo studies. Endoscopic-OCT typically requires a section of the sample arm fiber to be scanned during image acquisition, which produces a dynamically changing polarization state of light incident on the sample. Here, we demonstrate the effects of linear-scanning, and rotary-scanning probes in the sample arm of a PS-OCT system, and demonstrate the necessary modifications to be made for successful endoscopic PS-OCT imaging.

Characterizing and quantifying noise sources in birefringence imaging with polarization-sensitive optical coherence tomography (PS-OCT) is necessary for the development of efficient noise reduction techniques for real-time clinical PS-OCT imaging. We propose three noise regimes based on the strength of specimen backscattering and dominated by different noise sources. We introduce a model that predicts noise effects in two regimes. The model includes source/detector intensity noise, and couples speckle effects with the longitudinal delays due to instrument and specimen birefringence to create realistic noise on simulated orthogonal interference fringe amplitudes and on their relative phases. Experimental examples of the three regimes are presented and in two of them, qualitative agreement between the model and experimental data is demonstrated.

Polarization sensitive Fourier domain optical coherence tomography (PS-FD-OCT) using fiber components with continuous polarization modulation is demonstrated.
The incident polarized light is modulated by electro-optic modulator (EO modulator) synchronized with lateral B-scanning.
By the incident polarization modulation and the polarization sensitive spectrometer, the depth-resolved Jones matrix image of biological sample can be measured.
This method uses both polarization modulation method and Fourier transform method.
In this paper, the algorithm is described and the phase retardation image of chicken breast muscle is measured.

National Health Interview Survey (NHIS) estimates more than 1.1 million burn injuries per year in the United States, with nearly 15,000 fatalities from wounds and related complications. An imaging modality capable of evaluating burn depths non-invasively is the polarization-sensitive optical coherence tomography. We report on the use of a high-speed, fiber-based Mueller-matrix OCT system with continuous source-polarization modulation for burn depth evaluation. The new system is capable of imaging at near video-quality frame rates (8 frames per second) with resolution of 10 μm in biological tissue (index of refraction: 1.4) and sensitivity of 78 dB. The sample arm optics is integrated in a hand-held probe simplifying the in vivo experiments. The applicability of the system for burn depth determination is demonstrated using biological samples of porcine tendon and porcine skin. The results show an improved imaging depth (1 mm in tendon) and a clear localization of the thermally damaged region. The burnt area determined from OCT images compares well with the histology, thus proving the system's potential for burn depth determination.

Polarization-sensitive optical coherence tomography has been used to spatially map the birefringence of equine articular cartilage. The polar orientation of the collagen fibers relative to the plane of the joint surface must be taken into account if a quantitative measurement of true birefringence is required. Using a series of images taken at different angles of illumination, we determine the fiber polar angle and true birefringence at one site on a sample of equine cartilage, on the assumption that the fibers lie within the plane of imaging. We propose a more general method based on the extended Jones matrix formalism to determine both the polar and azimuthal orientation of the collagen fibers as well as the true
birefringence as functions of depth.

Menisci are frequently injured. A small meniscus tear may progress to a deeper tear if not treated. We will present the capability of diagnosis of meniscus injuries with OCT and PSOCT and the performance improvement of OCT that benefits from both local birefringence imaging and 3-dimensional reconstructions.

In this paper, the polarization sensitivity of articular cartilage was investigated by using polarization sensitivity optical coherence tomography (PS-OCT) obtained by varying the angel of incident illumination. Experimental results show that when the incident light is perpendicular to the tissue surface, normal articular cartilage demonstrates little polarization sensitivity. Significant variations in birefringence of articular cartilage observed when the angle of incident light was adjusted between 0° and 90° relative to the tissue surface. Directional polarization sensitivity of articular cartilage as obtained by PS-OCT imaging using variations in the angle of incident illumination can be used to access the orientation and organization of the collagen matrix of these tissues. The polarization sensitivity and the birefringence images obtained can be explained by the angle of illumination relative to the unique microstructure and orientation of the collagen fibrils and fibers of articular cartilage.

We have developed a novel noise model for the analysis of speckle noise and accuracy in birefringence imaging with polarization sensitive optical coherence tomography. Analytical expressions for the signal and noise in Stokes vectors are found, and these are used to investigate the uncertainty in the estimation of amplitude and orientation of birefringence. The important parameter in the model is the correlation between local reflectivity of the two orthogonal polarizations.